Boxes start to matter when you sell your stuff as near new. Other than that, i think it is only important that you have all the parts and pack it safely if shipping.
I dont know about Pentax, but i think the warranty should be accepted even without the box.
Another thing might be unique, special, almost collectable items. Something along the lines of famous limited's, or 50/1.2. Where you'd like to have all that came with it.
I, for example got 70/2.4 for less than half of the price. Optically and mechanically it is perfect, but the rear cap is not even Pentax, some of the paint has worn of and it came without the nice pouch or anything else. Bare lens and caps.
That takes away a lot of the limited feel. Luckly it does the same with the price. Still, the pictures are outstanding.
I would not apply a hard 90% reduction to each item. Evaluate all of them separately. Take a look in the ebay. Visit this site:
http://kmp.bdimitrov.de/
And see what does he says about the availability of the item under question.
For example such lenses as FA 50/1.4 cost several times more than they did year ago. So you could actually sell it for more than you bought it, still being under 90% of brand new price.
For other items the price savings of 10% may not be significant enough to choose over a brand new, in a box, full time warranty product.